Thermodynamics of the glucocorticoid receptor-DNA interaction: Binding of wild-type GR DBD to different response elements

Lundbäck, Thomas; Cairns, Carol; Gustafsson, J; Carlstedt‐Duke, Jan; Härd, Torleif

doi:10.1021/bi00070a015

Cited by 53 publications

(44 citation statements)

References 35 publications

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“…Therefore, although the near-0 value of AC:,o for the wild-type DNA binding to dHSF(33-163) suggests that minimal changesin polypeptide conformation occur upon DNA binding, this is probably not the case for the binding of the mutant DNA. The near-0 value of AC: for the binding of the wild-type DNA is in contrast to recent studies on sequence-specific protein-DNA interactions, which do show such temperature dependence Jin et al, 1993;Lundback et al, 1993;Spolar & Record, 1994). It should be noted, however, that reactants used in these studies were of different size and had different stoichiometries than those studied here.…”

Section: Analysis Of Thermodynamic Parameters Characterizing the Intecontrasting

confidence: 97%

Interaction of the DNA‐binding domain of Drosophila heat shock factor with its cognate DNA site: A thermodynamic analysis using analytical ultracentrifugation

et al. 1994

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Heat shock transcription factor (HSF) mediates the activation of heat shock genes by binding to its cognate sites with high affinity and specificity. The high-affinity binding of HSF is dependent on the formation of an HSF homotrimer, which interacts specificaIIy with the heat shock response element (HSE), comprised of 3 inverted repeats of the 5-bp sequence NGAAN. In order to investigate the thermodynamic basis of the interaction between HSF and HSE, we have overexpressed and purified a polypeptide (dHSF(33-163)) encompassing only the DNA-binding domain of HSF from Drosophila and analyzed its binding to DNA by equilibrium analytical ultracentrifugation using a multiwavelength scan technique. We demonstrate that dHSF(33-163) can bind as a monomer with 1:l stoichiometry to a synthetic 13-bp DNA containing a single NGAAN sequence. The values of the thermodynamic parameters obtained from the temperature dependence of the equilibrium binding constants indicate that the changes of free energy for the binding of dHSF(33-163) to the wild-type site and a mutant DNA site are predominantly characterized by substantial negative changes of enthalpy. Binding to the wild-type DNA is characterized by a significant positive change of entropy, whereas binding to the mutant DNA is distinguished by a negative change of entropy of comparable magnitude. The binding to the mutant DNA was also highly sensitive to increasing salt concentrations, indicating a dominance of ionic interactions. The sequence-specific, 1: 1 binding of dHSF to the NGAAN sequence provides a basis for the analysis of higher order interactions between HSF trimers and the HSE. Keywords: HSE; HSF; protein-DNA interactions; ultracentrifugal analysisThe transcriptional induction of heat shock genes in eukaryotes is initiated by the binding of the transcription factor heat shock factor (HSF) to its cognate site, the heat shock element (HSE), which is composed of 3 contiguous repeats of the 5-bp sequence NGAAN arranged in alternating orientation: 5'- [NGAAN] [NTTCN][NGAAN]-3'. The high-affinity binding of HSF to a complete HSE is dependent on the formation of an HSF homotrimer (for a review, see Lis & Wu, 1993). Although the exact stoichiometry of the interaction between HSF subunits and the HSE has not been determined, each subunit of the HSF trimer is generally assumed to recognize 1 of the 3 NGAAN repeats of the HSE. Thus, the high-affinity binding of HSF is thought to result from the combined interactions of the DNA-binding domains of all 3 HSF subunits.Sequence analysis of cDNA clones encoding HSFs from a wide variety of species reveals 2 conserved regions in the N-terminal part of the HSF protein that represent the DNAbinding domain and trimerization domain. The overall sequence of the DNA-binding domain does not show extensive similarity to any known category of DNA-binding motif, and it was therefore anticipated that a determination of the structure of HSF should reveal a new motif for specific DNA recognition. However, recent X-ray and NMR studies ...

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Section: Analysis Of Thermodynamic Parameters Characterizing the Intecontrasting

confidence: 97%

Interaction of the DNA‐binding domain of Drosophila heat shock factor with its cognate DNA site: A thermodynamic analysis using analytical ultracentrifugation

et al. 1994

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“…Dependence (35). Although EII mtl is known to form dimers and, therefore, it could be argued that dimerization leads to the large value of ⌬C p o obs determined here, we do not believe that this is the case.…”

Section: Table III Perseitol Binding By Phosphorylated Eii Mtlmentioning

confidence: 57%

Thermodynamic Evidence for Conformational Coupling between the B and C Domains of the Mannitol Transporter of Escherichia coli, Enzyme IImtl

Meijberg

Schuurman-Wolters

Robillard³

1998

Journal of Biological Chemistry

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The transport across the cytoplasmic membrane and concomitant phosphorylation of mannitol in Escherichia coli is catalyzed by the mannitol-specific transport protein from the phosphoenolpyruvate-dependent phosphotransferase system, enzyme II mtl . Interactions between the cytoplasmic B and the membrane embedded C domain play an important role in the catalytic cycle of this enzyme, but the nature of this interaction is largely unknown. We have studied the thermodynamics of binding of (i) mannitol to enzyme II mtl , (ii) the substrate analog perseitol to enzyme II mtl , (iii) perseitol to phosphorylated enzyme II mtl , and (iv) mannitol to enzyme II mtl treated with trypsin to eliminate the cytoplasmic domains. Analysis of the heat capacity increment of these reactions showed that approximately 50 -60 residues are involved in the binding of mannitol and perseitol, but far less in the phosphorylated state or after removal of the B domain. A model is proposed in which binding of mannitol leads to the formation of a contact interface between the two domains, either by folding of unstructured parts or by docking of preexisting surfaces, thus positioning the incoming mannitol close to the phosphorylation site on the B domain to facilitate the transfer of the phosphoryl group.The transport of carbohydrates from the environment into the bacterial cell is, in many cases, accomplished by a complex of proteins that together make up the phosphoenolpyruvatedependent phosphotransferase system (PTS) 1 (1, 2). This system consists of a number of transport proteins, each one specific for one carbohydrate, and a chain of cytoplasmic proteins that ultimately transfer a phosphoryl group derived from PEP to the incoming carbohydrate. The first protein in this chain is enzyme I, which accepts the phosphoryl group from PEP and transfers it to HPr, which in its phosphorylated form is the substrate for the transport proteins. All transport proteins of the PTS have a similar architecture, consisting of a part that binds and transports the carbohydrate and is embedded in the cytoplasmic membrane and two cytoplasmic parts, responsible for the phosphorylation of the substrate. The parts may or may not be covalently bound, and all possible combinations do, in fact, exist. In the case of the mannitol-specific transporter from Escherichia coli, termed enzyme II mannitol , all three parts are covalently linked and are, thus, domains of the same protein.The phosphoryl group is accepted from P-HPr by His-554 in the C-terminal A domain and transferred to Cys-384 on the B domain. Mannitol is bound at the periplasmic side and translocated across the membrane by the N-terminal C domain, after which the carbohydrate is phosphorylated by the B domain. The protein is believed to function as a dimer, both in the membrane and solubilized in detergent (3-9).It is obvious from the above that domain interactions play an important role in the catalytic cycle of this enzyme. Lolkema et al. (10), for instance, have shown that phosphorylation of the B domain cau...

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“…This interaction between the two nonpolar substituents is the discriminating feature of specific steroid receptor-DNA interfaces, and the resulting dehydration of the protein-DNA interface contributes entropic stabilization to the binding (35,37). In the nonconsensus AR half-complex, A replaces the T at position 4 of the sense strand, resulting in the loss of the Val-564[23]-T4 contact.…”

Section: Resultsmentioning

confidence: 99%

Structural basis of androgen receptor binding to selective androgen response elements

Shaffer

Jivan

Dollins

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

347

336

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Steroid receptors bind as dimers to a degenerate set of response elements containing inverted repeats of a hexameric half-site separated by 3 bp of spacer (IR3). Naturally occurring selective androgen response elements have recently been identified that resemble direct repeats of the hexameric half-site (ADR3). The 3D crystal structure of the androgen receptor (AR) DNA-binding domain bound to a selective ADR3 reveals an unexpected head-tohead arrangement of the two protomers rather than the expected head-to-tail arrangement seen in nuclear receptors bound to response elements of similar geometry. Compared with the glucocorticoid receptor, the DNA-binding domain dimer interface of the AR has additional interactions that stabilize the AR dimer and increase the affinity for nonconsensus response elements. This increased interfacial stability compared with the other steroid receptors may account for the selective binding of AR to ADR3 response elements.T he androgen receptor (AR) is a ligand-activated transcription factor that plays a central role in male sexual development and in the etiology of prostate cancer (1, 2). It is a member of the steroid and nuclear hormone receptor superfamily, which also includes receptors for glucocorticoids (GR), mineralocorticoids (MR), progesterone (PR), estrogens (ER), and vitamin D (VDR) (3). Members of this family contain conserved, discrete, DNA-binding domains (DBDs) and ligand-binding domains. The amino-terminal domain and the hinge region connecting the central DBD to the C-terminal ligand-binding domain diverge among family members.The hormone receptor DBD consists of a highly conserved 66-residue core made up of two zinc-nucleated modules, shown schematically in Fig. 1 A (4, 5). With VDR as the only reported exception (6), the isolated DBD and associated C-terminal extension are necessary and sufficient to generate the same pattern of DNA response element selectivity, partner selection, and dimerization as the full-length receptor from which it is derived (6-11).Although ligand binding elicits distinct hormone-specific responses, all classical steroid receptors (AR, PR, MR, and GR) recognize identical DNA response elements, which consist of two hexameric half-sites (5Ј-AGAACA-3Ј) arranged as inverted repeats with 3 bp of separating DNA, producing the 2-fold IR3 sequence pattern (Fig. 1B) (12). A question that continues to engage the steroid receptor field is how these transcription factors achieve DNA target specificity despite this degeneracy. As seen in the structures of the GR and ER DBDs bound to IR3 elements (4, 13), the receptors bind as ''head-to-head'' homodimers whose symmetric displacement across the DNA pseudodyad reflects the underlying half-site arrangement. Differences in steroid metabolism, receptor expression, local chromatin structure, and the availability of cofactors all contribute to steroid-specific responses (14-17). However, recent work has now also identified selective androgen response elements (AREs). The AREs consist of two hexameric half-sites a...

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Thermodynamics of the glucocorticoid receptor-DNA interaction: Binding of wild-type GR DBD to different response elements

Cited by 53 publications

References 35 publications

Interaction of the DNA‐binding domain of Drosophila heat shock factor with its cognate DNA site: A thermodynamic analysis using analytical ultracentrifugation

Interaction of the DNA‐binding domain of Drosophila heat shock factor with its cognate DNA site: A thermodynamic analysis using analytical ultracentrifugation

Thermodynamic Evidence for Conformational Coupling between the B and C Domains of the Mannitol Transporter of Escherichia coli, Enzyme IImtl

Structural basis of androgen receptor binding to selective androgen response elements

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